Self-assembled monolayers (SAMs) of phosphonic acids (PAs) on transparent conductive oxide (TCO) surfaces can facilitate improvement in TCO/organic semiconductor interface properties. When ordered PA SAMs are formed on oxide substrates, interface dipole and electronic structure are affected by the functional group properties, orientation, and binding modes of the modifiers. Choosing octylphosphonic acid (OPA), F-13-octylphosphonic acid (F(13)OPA), pentafluorophenyl phosphonic acid (F(5)PPA), benzyl phosphonic acid (BnPA), and pentafluorobenzyl phosphonic acid (F(5)BnPA) as a representative group of modifiers, we report polarization modulation-infrared reflection absorption spectroscopy (PM-IRRAS) of binding and molecular orientation on indium-doped zinc oxide (IZO) substrates. Considerable variability in molecular orientation and binding type is observed with changes in PA functional group. OPA exhibits partially disordered alkyl chains but on average the chain axis is tilted similar to 57 degrees from the surface normal. F(13)OPA tilts 26 degrees with mostly tridentate binding. The F(5)PPA ring is tilted 23 degrees from the surface normal with a mixture of bidentate and tridentate binding; the BnPA ring tilts 31 degrees from normal with a mixture of bidentate and tridentate binding, and the FsBnPA ring tilts 58 degrees from normal with a majority of bidentate with some tridenate binding. These trends are consistent with what has been observed previously for the effects of fluorination on orientation of phosphonic acid modifiers. These results from PM-IRRAS are correlated with recent results on similar systems from near-edge X-ray absorption fine structure (NEXAFS) and density functional theory (DFT) calculations. Overall, these results indicate that both surface binding geometry and intermolecular interactions play important roles in dictating the orientation of PA modifiers on TCO surfaces. This work also establishes PMIRRAS as a routine method for SAM orientation determination on complex oxide substrates.